PDB-3epy: Crystal Structure of human acyl-CoA binding domain 7 complexed wi...

ID or keywords:

Entry

Database: PDB / ID: 3epy

Title

Crystal Structure of human acyl-CoA binding domain 7 complexed with palmitoyl-Coa

Components

Acyl-CoA-binding domain-containing protein 7

Keywords

LIPID BINDING PROTEIN / ACYL-COA BINDING PROTEIN / FATTY ACID / LIPID METABOLISM / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

fatty-acyl-CoA binding / Mitochondrial Fatty Acid Beta-Oxidation / fatty acid metabolic process
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.005 Å

Authors

Kavanagh, K.L. / Salah, E. / Yue, W.W. / Savitsky, P. / Murray, J.W. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Bountra, C. / von Delft, F. ...

Citation

Journal: To be Published
Title: Crystal Structure of human acyl-CoA binding domain 7 complexed with palmitoyl-Coa
Authors: Kavanagh, K.L. / Salah, E. / Yue, W.W. / Savitsky, P. / Murray, J.W. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Bountra, C. / von Delft, F. / Oppermann, U.

History

Deposition	Sep 30, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 20, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Jan 31, 2018	Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3epy.cif.gz	88.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3epy.ent.gz	67.3 KB	Display	PDB format
PDBx/mmJSON format	3epy.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3epy_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	3epy_full_validation.pdf.gz	1.4 MB	Display
Data in XML	3epy_validation.xml.gz	10.9 KB	Display
Data in CIF	3epy_validation.cif.gz	13.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ep/3epy ftp://data.pdbj.org/pub/pdb/validation_reports/ep/3epy	HTTPS FTP

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Related structure data

Related structure data	2cb8S S: Starting model for refinement
Similar structure data	2770 4wn4-d 7btc-d 1kzq-d 1kyq-2 4ud7-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#147 - Mar 2012 Rhodopsin similarity (1) #134 - Feb 2011 Integrin similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #100 - Apr 2008 Adrenergic Receptors similarity (1) #164 - Aug 2013 Serotonin Receptor similarity (1) #171 - Mar 2014 Neurotransmitter Transporters similarity (1) #27 - Mar 2002 Bacteriorhodopsin similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

PDB pages

PDBj /

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NCBI

Related items in Molecule of the Month

#147 - Mar 2012
Rhodopsin
similarity (1)
#134 - Feb 2011
Integrin
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#93 - Sep 2007
Citrate Synthase
similarity (1)
#100 - Apr 2008
Adrenergic Receptors
similarity (1)
#164 - Aug 2013
Serotonin Receptor
similarity (1)
#171 - Mar 2014
Neurotransmitter Transporters
similarity (1)
#27 - Mar 2002
Bacteriorhodopsin
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#216 - Dec 2017
Biodegradable Plastic
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)

Deposited unit

A: Acyl-CoA-binding domain-containing protein 7

B: Acyl-CoA-binding domain-containing protein 7

hetero molecules

21.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Acyl-CoA-binding domain-containing protein 7

B: Acyl-CoA-binding domain-containing protein 7

hetero molecules

A: Acyl-CoA-binding domain-containing protein 7

B: Acyl-CoA-binding domain-containing protein 7

hetero molecules

defined by software
43.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	114.515, 27.922, 60.437
Angle α, β, γ (deg.)	90.00, 102.79, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain A and backbone and resid 3:16
2	1	1	chain B and backbone and resid 3:16
1	1	2	chain A and sidechain and resid 3:16
2	1	2	chain B and sidechain and resid 3:16
1	1	3	chain A and backbone and resid 17:29
2	1	3	chain B and backbone and resid 17:29
1	1	4	chain A and sidechain and resid 17:29
2	1	4	chain B and sidechain and resid 17:29
1	1	5	chain A and backbone and resid 30:41
2	1	5	chain B and backbone and resid 30:41
1	1	6	chain A and sidechain and resid 30:41
2	1	6	chain B and sidechain and resid 30:41
1	1	7	chain A and backbone and resid 42:57
2	1	7	chain B and backbone and resid 42:57
1	1	8	chain A and sidechain and resid 42:57
2	1	8	chain B and sidechain and resid 42:57
1	1	9	chain A and backbone and resid 58:65
2	1	9	chain B and backbone and resid 58:65
1	1	10	chain A and sidechain and resid 58:65
2	1	10	chain B and sidechain and resid 58:65
1	1	11	chain A and backbone and resid 66:80
2	1	11	chain B and backbone and resid 66:80
1	1	12	chain A and sidechain and resid 66:80
2	1	12	chain B and sidechain and resid 66:80
1	1	13	chain A and backbone and resid 81:88
2	1	13	chain B and backbone and resid 81:88
1	1	14	chain A and sidechain and resid 81:88
2	1	14	chain B and sidechain and resid 81:88

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

Details

DIMER

#1: Protein	Acyl-CoA-binding domain-containing protein 7 Mass: 9892.368 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACBD7 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8N6N7
#2: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#3: Chemical	ChemComp-PLM / PALMITIC ACID Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₆H₃₂O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.35 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG3350, 0.2 M MgCl2, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97243 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 26, 2008
Radiation	Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97243 Å / Relative weight: 1
Reflection	Resolution: 2→25 Å / Num. all: 12725 / Num. obs: 12725 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / B_iso Wilson estimate: 30 Å² / R_merge(I) obs: 0.092 / Net I/σ(I): 8.6
Reflection shell	Resolution: 2→2.11 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.566 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1834 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
MAR345		data collection
PHASER		phasing
PHENIX	(phenix.refine)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2cb8

2cb8

Resolution: 2.005→24.126 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2572	631	5.09 %	random
R_work	0.2032	-	-	-
all	0.2059	-	-	-
obs	0.2059	12400	96.25 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 63.568 Å² / k_sol: 0.39 e/Å³

Refinement step

Cycle: LAST / Resolution: 2.005→24.126 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1296	0	94	86	1476

Refine LS restraints

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	f_bond_d	0.007
X-RAY DIFFRACTION	f_angle_deg	1.075

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	56	X-RAY DIFFRACTION	POSITIONAL
1	2	B	56	X-RAY DIFFRACTION	POSITIONAL	0.033
2	1	A	41	X-RAY DIFFRACTION	POSITIONAL
2	2	B	41	X-RAY DIFFRACTION	POSITIONAL	0.361
3	1	A	52	X-RAY DIFFRACTION	POSITIONAL
3	2	B	52	X-RAY DIFFRACTION	POSITIONAL	0.03
4	1	A	49	X-RAY DIFFRACTION	POSITIONAL
4	2	B	49	X-RAY DIFFRACTION	POSITIONAL	0.246
5	1	A	48	X-RAY DIFFRACTION	POSITIONAL
5	2	B	48	X-RAY DIFFRACTION	POSITIONAL	0.034
6	1	A	46	X-RAY DIFFRACTION	POSITIONAL
6	2	B	46	X-RAY DIFFRACTION	POSITIONAL	0.124
7	1	A	64	X-RAY DIFFRACTION	POSITIONAL
7	2	B	64	X-RAY DIFFRACTION	POSITIONAL	0.033
8	1	A	53	X-RAY DIFFRACTION	POSITIONAL
8	2	B	53	X-RAY DIFFRACTION	POSITIONAL	0.159
9	1	A	32	X-RAY DIFFRACTION	POSITIONAL
9	2	B	32	X-RAY DIFFRACTION	POSITIONAL	0.038
10	1	A	30	X-RAY DIFFRACTION	POSITIONAL
10	2	B	30	X-RAY DIFFRACTION	POSITIONAL	0.223
11	1	A	60	X-RAY DIFFRACTION	POSITIONAL
11	2	B	60	X-RAY DIFFRACTION	POSITIONAL	0.036
12	1	A	41	X-RAY DIFFRACTION	POSITIONAL
12	2	B	41	X-RAY DIFFRACTION	POSITIONAL	0.189
13	1	A	32	X-RAY DIFFRACTION	POSITIONAL
13	2	B	32	X-RAY DIFFRACTION	POSITIONAL	0.03
14	1	A	29	X-RAY DIFFRACTION	POSITIONAL
14	2	B	29	X-RAY DIFFRACTION	POSITIONAL	0.17

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.0053-2.16	0.3233	126	0.2523	2178	X-RAY DIFFRACTION	90
2.16-2.3772	0.289	121	0.2156	2291	X-RAY DIFFRACTION	96
2.3772-2.7208	0.2875	128	0.2254	2374	X-RAY DIFFRACTION	98
2.7208-3.4263	0.2726	130	0.2019	2408	X-RAY DIFFRACTION	98
3.4263-24.128	0.2159	126	0.1852	2518	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	5.354	-6.096	-2.3497	6.4524	1.7964	0.8251	-0.0654	-0.3126	0.2233	-0.0157	0.1909	-0.5962	-0.1055	0.0393	-0.1115	0.2046	0.0648	0.0198	0.2031	0.0169	0.2166	73.0898	17.0693	-18.0876
2	3.4968	-1.1529	-1.9688	0.1354	0.0007	5.763	0.2888	0.1371	0.2182	-0.2693	0.1822	-0.1179	-0.0664	-0.1753	-0.3154	0.2037	0.0228	-0.0332	0.2108	0.0304	0.1588	58.5407	30.4593	-12.429
3	2.7155	0.9087	-2.5716	6.5407	-2.3013	1.6236	-0.0474	0.5634	-0.1703	-0.4718	0.0149	-0.5584	0.1722	-0.3016	0.0089	0.0937	-0.0359	-0.0085	0.2155	-0.0717	0.1379	65.9593	29.6948	7.1129
4	-1.6721	1.1685	-0.2225	9.1875	1.5055	1.8936	0.247	-0.1114	-0.5625	0.6436	0.0331	-1.8998	0.1873	-0.002	-0.2016	0.1847	-0.0742	-0.1975	0.2427	0.0794	0.5998	79.7024	35.786	19.361
5	0.2154	-0.4872	0.1372	2.2349	1.6687	-0.2596	-0.0472	-0.0889	-0.0859	0.4922	-0.1685	0.6433	0.8799	-0.6841	0.2315	0.6513	-0.0295	0.1688	0.3533	0.07	0.3864	65.6246	14.8997	-13.655
6	3.7438	-0.7639	-1.4991	6.3143	-0.7121	1.0375	-0.254	0.367	0.1025	-1.2154	1.0101	0.0451	0.4157	-0.0923	-0.299	0.3438	-0.1671	-0.0163	0.3488	0.1394	0.3176	71.7764	13.8043	-12.2419
7	2.8556	-0.775	0.3955	2.1146	-0.1087	0.7681	0.0411	0.0847	-0.1773	0.2362	-0.0719	-0.4126	-0.1318	0.1325	0.0234	0.264	-0.1175	-0.0626	0.1564	0.0103	0.2309	73.9015	38.5085	17.3077
8	4.8095	4.8802	3.7443	4.2529	6.6228	9.0949	0.4336	-0.228	-0.3557	0.6089	0.0228	-0.0046	0.9625	-0.5385	-0.2013	0.2013	-0.0358	0.0339	0.1815	-0.003	0.2038	58.9949	24.9755	12.2978
9	0.7068	-0.2592	2.7474	8.8183	-5.6097	7.7086	-0.1892	-0.3087	0.3453	0.6145	-0.1763	-0.8189	-0.8132	-1.0277	0.3949	0.1003	0.0172	0.0155	0.2572	-0.0883	0.168	65.6921	25.7044	-7.4786
10	1.2738	-5.3232	-1.1135	5.8909	2.1555	1.8489	0.0664	-0.7115	1.3087	-0.342	0.3614	-2.9168	-0.2759	-0.1064	-0.5614	0.2256	0.0503	0.1761	0.1904	0.0629	0.7678	78.3148	19.7378	-20.318
11	1.6517	-0.8362	-1.2994	3.475	3.8302	8.0911	-1.444	0.0581	0.1074	0.0518	-0.7416	1.9341	-0.5689	-1.8137	1.5398	0.3813	0.0165	-0.1221	0.5284	-0.1161	0.6029	66.1915	40.5326	13.5943
12	3.5708	-8.356	0.1069	-5.457	3.7667	2.1639	-0.082	-0.031	1.2158	0.4502	1.3028	-0.0607	0.7487	0.2094	-0.7645	0.3146	-0.0298	-0.0343	0.4949	0.0563	0.315	73.4413	43.4176	12.1005

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and resid 1:38
2	X-RAY DIFFRACTION	2	chain A and resid 39:46
3	X-RAY DIFFRACTION	3	chain A and resid 47:66
4	X-RAY DIFFRACTION	4	chain A and resid 67:88
5	X-RAY DIFFRACTION	5	chain A and resid 100
6	X-RAY DIFFRACTION	6	chain A and resid 101
7	X-RAY DIFFRACTION	7	chain B and resid 3:38
8	X-RAY DIFFRACTION	8	chain B and resid 39:46
9	X-RAY DIFFRACTION	9	chain B and resid 47:66
10	X-RAY DIFFRACTION	10	chain B and resid 67:88
11	X-RAY DIFFRACTION	11	chain B and resid 100
12	X-RAY DIFFRACTION	12	chain B and resid 101

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